Managing a Nextstrain Installation

This page is for users who have already finished Installing Nextstrain.

Steps vary by runtime option (Docker, Conda, ambient). To determine which Nextstrain runtime you are using, run:

nextstrain version --verbose

and look for the name that has (default) next to it.

Update an existing installation

Update the Docker runtime:

nextstrain update docker

If the output notes that an update of the Nextstrain CLI itself is available, run the suggested command (after optionally reviewing the release notes).

Troubleshoot a broken installation

Running nextstrain check-setup docker will also report potential issues. Make sure there are no errors or warnings reported.

The Docker runtime requires that the Docker service is running on your computer behind the scenes. If you see a message like:

Cannot connect to the Docker daemon at […]. Is the docker daemon running?

Then it is likely that the Docker service is not running. On macOS and Windows, try quitting Docker Desktop (if it’s open) and restarting it. On Linux, try running sudo systemctl restart docker.

If you the above isn’t sufficient and you need more help troubleshooting, please post to our discussion forum where members of the community and the Nextstrain team can help out.


We do not have an automated uninstall process currently. Instead, follow these manual steps:

  1. If the directory ~/.nextstrain exists, remove it.

  2. If using the Docker runtime, remove all nextstrain/… Docker images:

    docker image rm $(docker image ls -q "nextstrain/*")

    Optionally, uninstall Docker if only used for Nextstrain.

  3. If using the ambient runtime, remove the custom Conda environment:

    conda env remove -n <your-environment-name>

    Optionally, uninstall Conda if only used for Nextstrain.

  4. On Windows, optionally, uninstall WSL if only used for Nextstrain.